Developments in microarray-based detection devices have dramatically changed the biotechnology industry. The devices make it possible to analyze multiple biological samples simultaneously and detect rare transcripts in human. They also make it possible to obtain information from microarrays automatically within minutes instead of within months or even years without the help of the devices.
Microarrays typically comprise a plurality of polymers, such as oligonucleotides, peptides, and antibodies. The polymers are synthesized or deposited on a substrate in an array pattern, which can be labeled with optically detectable labels such as fluorescent tags or fluorophores. A typical microarray scanner uses laser as excitation light source, and use matching filters and photomultiplier tubes for detection. During scanning of a microarray, excitation light from the laser source hits different spots on the microarray. Fluorescent probes on the array emit Stokes-shifted light in response to the excitation light, and the emission light is collected by the photomultiplier tube. The resulting information on the microarray can be used for various purposes such as gene expression studies, mutational studies, genotyping, SNP studies, protein interaction analysis, as well as diagnosis and treatment of diseases.
The optical systems used in traditional microarray scanners use beam splitters to separate light beams. As shown in FIG. 1, laser light passes through laser light filter and projects on the beam splitter. Light reflected by the beam splitter then passes through the excitation objective lens, which focuses the light on the surface of the microarray chip. Fluorescent molecules on the microarray that are excited by the laser light emit fluorescent light, which is then collimated by the excitation objective lens and transmits through the beam splitter. Light transmitted through the beam splitter then passes the excitation light filter and become collected by the detector.
There are several drawbacks associated with traditional optical systems. First, incoming laser light loses energy by passing through the beam splitter. Accordingly, the intensity of the excitation light decreases, which in turn decreases the sensitivity of the system. Second, the glass surface of a traditional microarray chip usually reflects 1% or more of the incoming excitation light, which also enters the detection light path. Because in most microarray detection experiments the intensity of the emission light is millions of times weaker than the light intensity of the excitation laser light, light reflected from the glass slide poses significant background problems. Finally, because beam splitters are typically designed for a specific wavelength, they need to be adjusted whenever a new excitation light source is used or when multiple excitation light sources are used. This makes the design of the optical system difficult.